qiime 1.3.0-3 source package in Ubuntu


qiime (1.3.0-3) unstable; urgency=low

  [ Charles Plessy ]
  * renamed debian/upstream-metadata.yaml to debian/upstream

  [ Andreas Tille ]
  * Standards-Version: 3.9.3 (no changes needed)
  * debian/patches/ghc_7.4.2_compatibility.patch: Fix build problem based
    on illegal use of 'import System' (Thanks to Joachim Breitner
    <email address hidden>) for the patch
    Closes: #663889

 -- Andreas Tille <email address hidden>  Sat, 17 Mar 2012 19:19:38 +0100

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Uploaded by:
Debian Med on 2012-03-20
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Original maintainer:
Debian Med
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Low Urgency

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Series Pocket Published Component Section
Precise release on 2012-04-22 universe science


File Size SHA-256 Checksum
qiime_1.3.0-3.dsc 1.5 KiB 960ea1d441282e6c67615544a0b3249386cd39c11c9125702af51ab8879bf3ca
qiime_1.3.0.orig.tar.gz 7.5 MiB 4cad294f4e50c33c919ee862c8494cdf24a920aa755b3288b07d3a50bbf38fb5
qiime_1.3.0-3.debian.tar.gz 10.7 KiB 19341b648c309b760d89d2be2c5ac2480c034fdb1ae5fcff54e71788cd33c477

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Binary packages built by this source

qiime: Quantitative Insights Into Microbial Ecology

 QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
 microbial community analysis that integrates many third party tools which
 have become standard in the field. A standard QIIME analysis begins with
 sequence data from one or more sequencing platforms, including
  * Sanger,
  * Roche/454, and
  * Illumina GAIIx.
 With all the underlying tools installed,
 of which not all are yet available in Debian (or any other Linux
 distribution), QIIME can perform
  * library de-multiplexing and quality filtering;
  * denoising with PyroNoise;
  * OTU and representative set picking with uclust, cdhit, mothur, BLAST,
    or other tools;
  * taxonomy assignment with BLAST or the RDP classifier;
  * sequence alignment with PyNAST, muscle, infernal, or other tools;
  * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
  * alpha diversity and rarefaction, including visualization of results,
    using over 20 metrics including Phylogenetic Diversity, chao1, and
    observed species;
  * beta diversity and rarefaction, including visualization of results,
    using over 25 metrics including weighted and unweighted UniFrac,
    Euclidean distance, and Bray-Curtis;
  * summarization and visualization of taxonomic composition of samples
    using pie charts and histograms
 and many other features.
 QIIME includes parallelization capabilities for many of the
 computationally intensive steps. By default, these are configured to
 utilize a mutli-core environment, and are easily configured to run in
 a cluster environment. QIIME is built in Python using the open-source
 PyCogent toolkit. It makes extensive use of unit tests, and is highly
 modular to facilitate custom analyses.

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